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Takeya T, Yamakita M, Hayashi D, Fujisawa K, Sakai Y, Yurimoto H. Methanol production by reversed methylotrophy constructed in Escherichia coli. Biosci Biotechnol Biochem 2020; 84:1062-1068. [PMID: 31942827 DOI: 10.1080/09168451.2020.1715202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We constructed a reversed methylotrophic pathway that produces methanol, a promising feedstock for production of useful compounds, from fructose 6-phosphate (F6P), which can be supplied by catabolism of biomass-derived sugars including glucose, by a synthetic biology approach. Using Escherichia coli as an expression host, we heterologously expressed genes encoding methanol utilization enzymes from methylotrophic bacteria, i.e. the NAD+-dependent methanol dehydrogenase (MDH) from Bacillus methanolicus S1 and an artificial fusion enzyme of 3-hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase from Mycobacterium gastri MB19 (HPS-PHI). We confirmed that these enzymes can catalyze reverse reactions of methanol oxidation and formaldehyde fixation. The engineered E. coli strain co-expressing MDH and HPS-PHI genes produced methanol in resting cell reactions not only from F6P but also from glucose. We successfully conferred reversed methylotrophy to E. coli and our results provide a proof-of-concept for biological methanol production from biomass-derived sugar compounds.
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Affiliation(s)
- Tomoyuki Takeya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Miyabi Yamakita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Daisuke Hayashi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kento Fujisawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Wang Y, Fan L, Tuyishime P, Zheng P, Sun J. Synthetic Methylotrophy: A Practical Solution for Methanol-Based Biomanufacturing. Trends Biotechnol 2020; 38:650-666. [PMID: 31932066 DOI: 10.1016/j.tibtech.2019.12.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022]
Abstract
The increasing availability and affordability of natural gas has renewed interest in using methanol for bioproduction of useful chemicals. Engineering synthetic methylotrophy based on natural or artificial methanol assimilation pathways and genetically tractable platform microorganisms for methanol-based biomanufacturing is drawing particular attention. Recently, intensive efforts have been devoted to demonstrating the feasibility and improving the efficiency of synthetic methylotrophy. Various fuel, bulk, and fine chemicals have been synthesized using methanol as a feedstock. However, fully synthetic methylotrophs utilizing methanol as the sole carbon source and commercially viable bioproduction from methanol remain to be developed. Here, we review ongoing efforts to identify limiting factors, optimize synthetic methylotrophs, and implement methanol-based biomanufacturing. Future challenges and prospects are also discussed.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Philibert Tuyishime
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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53
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Carrillo M, Wagner M, Petit F, Dransfeld A, Becker A, Erb TJ. Design and Control of Extrachromosomal Elements in Methylorubrum extorquens AM1. ACS Synth Biol 2019; 8:2451-2456. [PMID: 31584803 PMCID: PMC6862569 DOI: 10.1021/acssynbio.9b00220] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Genetic
tools are a prerequisite to engineer cellular factories
for synthetic biology and biotechnology. Methylorubrum extorquens AM1 is an important platform organism of a future C1-bioeconomy.
However, its application is currently limited by the availability
of genetic tools. Here we systematically tested repABC regions to maintain extrachromosomal DNA in M. extorquens. We used three elements to construct mini-chromosomes that are stably
inherited at single copy number and can be shuttled between Escherichia coli and M. extorquens. These mini-chromosomes are compatible among each other and with
high-copy number plasmids of M. extorquens.
We also developed a set of inducible promoters of wide expression
range, reaching levels exceeding those currently available, notably
the PmxaF-promoter. In
summary, we provide a set of tools to control the dynamic expression
and copy number of genetic elements in M. extorquens, which opens new ways to unleash the metabolic and biotechnological
potential of this organism for future applications.
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Affiliation(s)
- Martina Carrillo
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Marcel Wagner
- LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Florian Petit
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Amelie Dransfeld
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
| | - Tobias J. Erb
- Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- LOEWE Center for Synthetic Microbiology, 35043 Marburg, Germany
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Belkhelfa S, Roche D, Dubois I, Berger A, Delmas VA, Cattolico L, Perret A, Labadie K, Perdereau AC, Darii E, Pateau E, de Berardinis V, Salanoubat M, Bouzon M, Döring V. Continuous Culture Adaptation of Methylobacterium extorquens AM1 and TK 0001 to Very High Methanol Concentrations. Front Microbiol 2019; 10:1313. [PMID: 31281294 PMCID: PMC6595629 DOI: 10.3389/fmicb.2019.01313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
The bio-economy relies on microbial strains optimized for efficient large scale production of chemicals and fuels from inexpensive and renewable feedstocks under industrial conditions. The reduced one carbon compound methanol, whose production does not involve carbohydrates needed for the feed and food sector, can be used as sole carbon and energy source by methylotrophic bacteria like Methylobacterium extorquens AM1. This strain has already been engineered to produce various commodity and high value chemicals from methanol. The toxic effect of methanol limits its concentration as feedstock to 1% v/v. We obtained M. extorquens chassis strains tolerant to high methanol via adaptive directed evolution using the GM3 technology of automated continuous culture. Turbidostat and conditional medium swap regimes were employed for the parallel evolution of the recently characterized strain TK 0001 and the reference strain AM1 and enabled the isolation of derivatives of both strains capable of stable growth with 10% methanol. The isolates produced more biomass at 1% methanol than the ancestor strains. Genome sequencing identified the gene metY coding for an O-acetyl-L-homoserine sulfhydrylase as common target of mutation. We showed that the wildtype enzyme uses methanol as substrate at elevated concentrations. This side reaction produces methoxine, a toxic homolog of methionine incorporated in polypeptides during translation. All mutated metY alleles isolated from the evolved populations coded for inactive enzymes, designating O-acetyl-L-homoserine sulfhydrylase as a major vector of methanol toxicity. A whole cell transcriptomic analysis revealed that genes coding for chaperones and proteases were upregulated in the evolved cells as compared with the wildtype, suggesting that the cells had to cope with aberrant proteins formed during the adaptation to increasing methanol exposure. In addition, the expression of ribosomal proteins and enzymes related to energy production from methanol like formate dehydrogenases and ATP synthases was boosted in the evolved cells upon a short-term methanol stress. D-lactate production from methanol by adapted cells overexpressing the native D-lactate dehydrogenase was quantified. A significant higher lactate yield was obtained compared with control cells, indicating an enhanced capacity of the cells resistant to high methanol to assimilate this one carbon feedstock more efficiently.
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Affiliation(s)
- Sophia Belkhelfa
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Ivan Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Anne Berger
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Valérie A Delmas
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Laurence Cattolico
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Alain Perret
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Aude C Perdereau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Ekaterina Darii
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Emilie Pateau
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Véronique de Berardinis
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Marcel Salanoubat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France
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55
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Wendisch VF. Metabolic engineering advances and prospects for amino acid production. Metab Eng 2019; 58:17-34. [PMID: 30940506 DOI: 10.1016/j.ymben.2019.03.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/18/2022]
Abstract
Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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56
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Ochsner AM, Hemmerle L, Vonderach T, Nüssli R, Bortfeld-Miller M, Hattendorf B, Vorholt JA. Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1. Mol Microbiol 2019; 111:1152-1166. [PMID: 30653750 PMCID: PMC6850437 DOI: 10.1111/mmi.14208] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2019] [Indexed: 01/03/2023]
Abstract
Until recently, rare‐earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca2+‐dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred methanol dehydrogenase in the presence of sufficient amounts of REE. Using reporter assays and a suppressor screen, we found that lanthanum (La3+) is sensed both in a XoxF‐dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsisthaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 identified XoxF as a top induced protein in planta and a core set of La3+‐regulated proteins under defined artificial media conditions. Among these was a REE‐binding protein that is encoded next to a gene for a TonB‐dependent transporter. The latter was essential for REE‐dependent growth on methanol indicating chelator‐assisted uptake of REEs.
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Affiliation(s)
- Andrea M Ochsner
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Thomas Vonderach
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Ralph Nüssli
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Bodo Hattendorf
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
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57
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Wang X, Wang X, Lu X, Ma C, Chen K, Ouyang P. Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:17. [PMID: 30679956 PMCID: PMC6340170 DOI: 10.1186/s13068-019-1356-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/09/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Methanol has attracted increased attention as a non-food alternative carbon source to sugar for biological production of chemicals and fuels. Moreover, the high degree of reduction of methanol offers some advantages in increasing the production yields of NAD(P)H-dependent metabolites. Here, we demonstrate an example of methanol bioconversion with the aim of improving production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli. RESULTS A synthetic methylotrophic E. coli was engineered with a nicotinamide adenine dinucleotide (NAD+)-dependent methanol dehydrogenase (MDH) and ribulose monophosphate (RuMP) pathway. Regarding the limited MDH activity, the role of activator proteins in vivo was investigated, and the NudF protein was identified capable of improving MDH activity and triggering increased methanol metabolism. Using 13C-methanol-labeling experiments, we confirmed methanol assimilation in the methylotrophic E. coli. A cycling RuMP pathway for methanol assimilation was also demonstrated by detecting multiple labeled carbons for several compounds. Finally, using the NAD(P)H-dependent metabolite lysine as a test, the potential of methanol bioconversion to generate value-added metabolites was determined. To further characterize the benefit of methanol as the carbon source, extra NADH from methanol oxidation was engineered to generate NADPH to improve lysine biosynthesis by expression of the POS5 gene from Saccharomyces cerevisiae, which resulted in a twofold improvement of lysine production. Moreover, this new sink further pulled upstream methanol utilization. CONCLUSION Through engineering methanol metabolism, lysine biosynthesis, and NADPH regeneration pathway from NADH, the bioconversion of methanol to improve chemical synthesis was successfully achieved in methylotrophic E. coli.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Xuelin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Xiaolu Lu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Chen Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816 Jiangsu China
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58
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Marino T, Prejanò M, Russo N. How Metal Coordination in the Ca-, Ce-, and Eu-Containing Methanol Dehydrogenase Enzymes Can Influence the Catalysis: A Theoretical Point of View. TRANSITION METALS IN COORDINATION ENVIRONMENTS 2019. [DOI: 10.1007/978-3-030-11714-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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59
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Fan L, Wang Y, Tuyishime P, Gao N, Li Q, Zheng P, Sun J, Ma Y. Engineering Artificial Fusion Proteins for Enhanced Methanol Bioconversion. Chembiochem 2018; 19:2465-2471. [DOI: 10.1002/cbic.201800424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/14/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Liwen Fan
- School of Life SciencesUniversity of Science and Technology of China Hefei 230026 China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Yu Wang
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Philibert Tuyishime
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ning Gao
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qinggang Li
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Ping Zheng
- School of Life SciencesUniversity of Science and Technology of China Hefei 230026 China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Jibin Sun
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Yanhe Ma
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
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60
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Burton M, Abanobi C, Wang KTC, Ma Y, Rasche ME. Substrate Specificity Analysis of Dihydrofolate/Dihydromethanopterin Reductase Homologs in Methylotrophic α-Proteobacteria. Front Microbiol 2018; 9:2439. [PMID: 30364315 PMCID: PMC6193120 DOI: 10.3389/fmicb.2018.02439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/24/2018] [Indexed: 12/22/2022] Open
Abstract
Methane-producing archaea and methylotrophic bacteria use tetrahydromethanopterin (H4MPT) and/or tetrahydrofolate (H4F) as coenzymes in one-carbon (C1) transfer pathways. The α-proteobacterium Methylobacterium extorquens AM1 contains a dihydromethanopterin reductase (DmrA) and two annotated dihydrofolate reductases (DfrA and DfrB). DmrA has been shown to catalyze the final step of H4MPT biosynthesis; however, the functions of DfrA and DfrB have not been examined biochemically. Moreover, sequence alignment (BLAST) searches have recognized scores of proteins that share up to 99% identity with DmrA but are annotated as diacylglycerol kinases (DAGK). In this work, we used bioinformatics and enzyme assays to provide insight into the phylogeny and substrate specificity of selected Dfr and DmrA homologs. In a phylogenetic tree, DmrA and homologs annotated as DAGKs grouped together in one clade. Purified histidine-tagged versions of the annotated DAGKs from Hyphomicrobium nitrativorans and M. nodulans (respectively, sharing 69 and 84% identity with DmrA) showed only low activity in phosphorylating 1,2-dihexanoyl-sn-glycerol when compared with a commercial DAGK from Escherichia coli. However, the annotated DAGKs successfully reduced a dihydromethanopterin analog (dihydrosarcinapterin, H2SPT) with kinetic values similar to those determined for M. extorquens AM1 DmrA. DfrA and DfrB showed little or no ability to reduce H2SPT under the conditions studied; however, both catalyzed the NADPH-dependent reduction of dihydrofolate. These results provide the first evidence that DfrA and DfrB function as authentic dihydrofolate reductases, while DAGKs with greater than 69% identity to DmrA may be misannotated and are likely to function in H4MPT biosynthesis.
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Affiliation(s)
- Mark Burton
- Department of Chemistry and Biochemistry, Center for Applied Biotechnology Studies, California State University, Fullerton, Fullerton, CA, United States
| | - Chidinma Abanobi
- Department of Chemistry and Biochemistry, Center for Applied Biotechnology Studies, California State University, Fullerton, Fullerton, CA, United States
| | - Kate Tzu-Chi Wang
- Department of Chemistry and Biochemistry, Center for Applied Biotechnology Studies, California State University, Fullerton, Fullerton, CA, United States
| | - Yihua Ma
- Department of Chemistry and Biochemistry, Center for Applied Biotechnology Studies, California State University, Fullerton, Fullerton, CA, United States
| | - Madeline E Rasche
- Department of Chemistry and Biochemistry, Center for Applied Biotechnology Studies, California State University, Fullerton, Fullerton, CA, United States
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Hani J, Abdel Nour G, Matta J, Jazzar B, Pfaffl MW, Hanna-Wakim L, Abdel Nour AM. Shisha microbiota: the good, the bad and the not so ugly. BMC Res Notes 2018; 11:446. [PMID: 29980232 PMCID: PMC6035416 DOI: 10.1186/s13104-018-3553-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/28/2018] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE Over the last decade, there has been a rapid expansion of the trendy water pipe smoking around the world especially among younger adults. The initial objective of this study was to identify the microbiota of the shisha, which may either be of no harm for the smoker or enhance the threat on his well-being. The total DNA for the metagenomics study was conducted on three different shishas from three different delivery shops in Jounieh, Lebanon. The microbiota in two solid parts of the shisha, shaft and hose, were analysed including the fresh tobacco and the water in the bowl. All samples were analysed using high-throughput sequencing of 16S rRNA gene amplicons. RESULTS Overall, more than 40 bacterial genera were found in the three investigated shishas, some are commensal others are pathogenic. All three shishas showed similar microbial content regarding the bacteria inhabiting in water, shaft, or hose. From the results of this study it appears that a very large quantity of bacteria was found in the water pipes, some are harmful and others beneficial. We assume that the presence of gut dependent microbiota is related to the loose hygienic conditions in which the shisha is prepared.
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Affiliation(s)
- Julia Hani
- Faculty of Agricultural and Food Sciences, The Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Ghenwa Abdel Nour
- Faculty of Agricultural and Food Sciences, The Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Joanne Matta
- Faculty of Agricultural and Food Sciences, The Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Boushra Jazzar
- Faculty of Agricultural and Food Sciences, The Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Michael W. Pfaffl
- Institute of Animal Physiology & Immunology, Faculty of Life Sciences, Technical University of Munich, Freising, Munich, Germany
| | - Lara Hanna-Wakim
- Faculty of Agricultural and Food Sciences, The Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Afif M. Abdel Nour
- Faculty of Agricultural and Food Sciences, The Holy Spirit University of Kaslik, Jounieh, Lebanon
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Lieven C, Herrgård MJ, Sonnenschein N. Microbial Methylotrophic Metabolism: Recent Metabolic Modeling Efforts and Their Applications In Industrial Biotechnology. Biotechnol J 2018; 13:e1800011. [PMID: 29917330 DOI: 10.1002/biot.201800011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/31/2018] [Indexed: 11/08/2022]
Abstract
Developing methylotrophic bacteria into cell factories that meet the chemical demand of the future could be both economical and environmentally friendly. Methane is not only an abundant, low-cost resource but also a potent greenhouse gas, the capture of which could help to reduce greenhouse gas emissions. Rational strain design workflows rely on the availability of carefully combined knowledge often in the form of genome-scale metabolic models to construct high-producer organisms. In this review, the authors present the most recent genome-scale metabolic models in aerobic methylotrophy and their applications. Further, the authors present models for the study of anaerobic methanotrophy through reverse methanogenesis and suggest organisms that may be of interest for expanding one-carbon industrial biotechnology. Metabolic models of methylotrophs are scarce, yet they are important first steps toward rational strain-design in these organisms.
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Affiliation(s)
- Christian Lieven
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nikolaus Sonnenschein
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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63
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Cui LY, Wang SS, Guan CG, Liang WF, Xue ZL, Zhang C, Xing XH. Breeding of Methanol-Tolerant Methylobacterium extorquens
AM1 by Atmospheric and Room Temperature Plasma Mutagenesis Combined With Adaptive Laboratory Evolution. Biotechnol J 2018; 13:e1700679. [DOI: 10.1002/biot.201700679] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/29/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Lan-Yu Cui
- MOE Key Lab of Industrial Biocatalysis; Department of Chemical Engineering; Tsinghua University; Tsinghua Yuan Street 100084 Beijing China
- School of Preclinical Medicine; Guangxi Medical University; Shuang Yong Road 530021 Nanning China
| | - Shan-Shan Wang
- MOE Key Lab of Industrial Biocatalysis; Department of Chemical Engineering; Tsinghua University; Tsinghua Yuan Street 100084 Beijing China
- College of Biological and Chemical Engineering; Anhui Polytechnic University; Beijing Middle Road 241000 Wuhu China
| | - Chang-Ge Guan
- MOE Key Lab of Industrial Biocatalysis; Department of Chemical Engineering; Tsinghua University; Tsinghua Yuan Street 100084 Beijing China
| | - Wei-Fan Liang
- MOE Key Lab of Industrial Biocatalysis; Department of Chemical Engineering; Tsinghua University; Tsinghua Yuan Street 100084 Beijing China
| | - Zheng-Lian Xue
- College of Biological and Chemical Engineering; Anhui Polytechnic University; Beijing Middle Road 241000 Wuhu China
| | - Chong Zhang
- MOE Key Lab of Industrial Biocatalysis; Department of Chemical Engineering; Tsinghua University; Tsinghua Yuan Street 100084 Beijing China
- Tsinghua University; Center for Synthetic and System Biology; Tsinghua Yuan Street 100084 Beijing China
| | - Xin-Hui Xing
- MOE Key Lab of Industrial Biocatalysis; Department of Chemical Engineering; Tsinghua University; Tsinghua Yuan Street 100084 Beijing China
- Tsinghua University; Center for Synthetic and System Biology; Tsinghua Yuan Street 100084 Beijing China
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64
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Schada von Borzyskowski L, Carrillo M, Leupold S, Glatter T, Kiefer P, Weishaupt R, Heinemann M, Erb TJ. An engineered Calvin-Benson-Bassham cycle for carbon dioxide fixation in Methylobacterium extorquens AM1. Metab Eng 2018; 47:423-433. [DOI: 10.1016/j.ymben.2018.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 10/17/2022]
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65
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N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization. J Proteomics 2018; 179:131-139. [DOI: 10.1016/j.jprot.2018.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 12/29/2022]
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66
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Meyer F, Keller P, Hartl J, Gröninger OG, Kiefer P, Vorholt JA. Methanol-essential growth of Escherichia coli. Nat Commun 2018; 9:1508. [PMID: 29666370 PMCID: PMC5904121 DOI: 10.1038/s41467-018-03937-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/22/2018] [Indexed: 12/22/2022] Open
Abstract
Methanol represents an attractive substrate for biotechnological applications. Utilization of reduced one-carbon compounds for growth is currently limited to methylotrophic organisms, and engineering synthetic methylotrophy remains a major challenge. Here we apply an in silico-guided multiple knockout approach to engineer a methanol-essential Escherichia coli strain, which contains the ribulose monophosphate cycle for methanol assimilation. Methanol conversion to biomass was stoichiometrically coupled to the metabolization of gluconate and the designed strain was subjected to laboratory evolution experiments. Evolved strains incorporate up to 24% methanol into core metabolites under a co-consumption regime and utilize methanol at rates comparable to natural methylotrophs. Genome sequencing reveals mutations in genes coding for glutathione-dependent formaldehyde oxidation (frmA), NAD(H) homeostasis/biosynthesis (nadR), phosphopentomutase (deoB), and gluconate metabolism (gntR). This study demonstrates a successful metabolic re-routing linked to a heterologous pathway to achieve methanol-dependent growth and represents a crucial step in generating a fully synthetic methylotrophic organism. Engineering synthetic methylotrophy remains challenging. Here, the authors engineer a methanol-essential E. coli by an in silico-guided multiple knockout approach and show a laboratory evolved strain can incorporate up to 24% methanol into core metabolites during growth.
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Affiliation(s)
- Fabian Meyer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Johannes Hartl
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Olivier G Gröninger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, 8093, Switzerland.
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67
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Schempp FM, Drummond L, Buchhaupt M, Schrader J. Microbial Cell Factories for the Production of Terpenoid Flavor and Fragrance Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2247-2258. [PMID: 28418659 DOI: 10.1021/acs.jafc.7b00473] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Terpenoid flavor and fragrance compounds are of high interest to the aroma industry. Microbial production offers an alternative sustainable access to the desired terpenoids independent of natural sources. Genetically engineered microorganisms can be used to synthesize terpenoids from cheap and renewable resources. Due to its modular architecture, terpenoid biosynthesis is especially well suited for the microbial cell factory concept: a platform host engineered for a high flux toward the central C5 prenyl diphosphate precursors enables the production of a broad range of target terpenoids just by varying the pathway modules converting the C5 intermediates to the product of interest. In this review typical terpenoid flavor and fragrance compounds marketed or under development by biotech and aroma companies are given, and the specificities of the aroma market are discussed. The main part of this work focuses on key strategies and recent advances to engineer microbes to become efficient terpenoid producers.
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Affiliation(s)
- Florence M Schempp
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Laura Drummond
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Markus Buchhaupt
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
| | - Jens Schrader
- DECHEMA-Forschungsinstitut, Industrial Biotechnology , Theodor-Heuss-Allee 25 , 60486 Frankfurt am Main , Germany
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68
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Jahn B, Pol A, Lumpe H, Barends TRM, Dietl A, Hogendoorn C, Op den Camp HJM, Daumann LJ. Similar but Not the Same: First Kinetic and Structural Analyses of a Methanol Dehydrogenase Containing a Europium Ion in the Active Site. Chembiochem 2018; 19:1147-1153. [PMID: 29524328 PMCID: PMC6100108 DOI: 10.1002/cbic.201800130] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Indexed: 01/23/2023]
Abstract
Since the discovery of the biological relevance of rare earth elements (REEs) for numerous different bacteria, questions concerning the advantages of REEs in the active sites of methanol dehydrogenases (MDHs) over calcium(II) and of why bacteria prefer light REEs have been a subject of debate. Here we report the cultivation and purification of the strictly REE-dependent methanotrophic bacterium Methylacidiphilum fumariolicum SolV with europium(III), as well as structural and kinetic analyses of the first methanol dehydrogenase incorporating Eu in the active site. Crystal structure determination of the Eu-MDH demonstrated that overall no major structural changes were induced by conversion to this REE. Circular dichroism (CD) measurements were used to determine optimal conditions for kinetic assays, whereas inductively coupled plasma mass spectrometry (ICP-MS) showed 70 % incorporation of Eu in the enzyme. Our studies explain why bacterial growth of SolV in the presence of Eu3+ is significantly slower than in the presence of La3+ /Ce3+ /Pr3+ : Eu-MDH possesses a decreased catalytic efficiency. Although REEs have similar properties, the differences in ionic radii and coordination numbers across the series significantly impact MDH efficiency.
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Affiliation(s)
- Bérénice Jahn
- Ludwig-Maximilians-Universität MünchenDepartment ChemieButenandtstr. 5–1381377MünchenGermany
| | - Arjan Pol
- Department of Microbiology, Institute of Wetland and Water ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Henning Lumpe
- Ludwig-Maximilians-Universität MünchenDepartment ChemieButenandtstr. 5–1381377MünchenGermany
| | - Thomas R. M. Barends
- Department of Biomolecular MechanismsMax-Planck Institute for Medical ResearchJahnstrasse 2969120HeidelbergGermany
| | - Andreas Dietl
- Department of Biomolecular MechanismsMax-Planck Institute for Medical ResearchJahnstrasse 2969120HeidelbergGermany
| | - Carmen Hogendoorn
- Department of Microbiology, Institute of Wetland and Water ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, Institute of Wetland and Water ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Lena J. Daumann
- Ludwig-Maximilians-Universität MünchenDepartment ChemieButenandtstr. 5–1381377MünchenGermany
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69
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Claassens NJ, Sánchez-Andrea I, Sousa DZ, Bar-Even A. Towards sustainable feedstocks: A guide to electron donors for microbial carbon fixation. Curr Opin Biotechnol 2018; 50:195-205. [PMID: 29453021 DOI: 10.1016/j.copbio.2018.01.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 12/31/2022]
Abstract
The replacement of fossil and agricultural feedstocks with sustainable alternatives for the production of chemicals and fuels is a societal and environmental necessity. This challenge can be tackled by using inorganic or one-carbon compounds as electron donors for microbial CO2 fixation and bioproduction. Yet, considering the wide array of microbial electron donors, which are the best suited for bioindustry? Here, we propose criteria to evaluate these compounds, considering factors such as production methods, physicochemical properties, and microbial utilization. H2, CO, and formate emerge as the most promising electron donors as they can be produced electrochemically at high efficiency and, importantly, have reduction potentials low enough to directly reduce the cellular electron carriers. Still, further research towards the production and utilization of other electron donors-especially phosphite-might unlock the full potential of microbial CO2 fixation and bioproduction.
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Affiliation(s)
- Nico Joannes Claassens
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Diana Zita Sousa
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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70
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Lee W, Kim S, Song I, Kwon Y, Park S, Oh BK, Oh HB, Lee J. Microbial production of uracil by an isolated Methylobacterium sp. WJ4 using methanol. Enzyme Microb Technol 2018; 111:63-66. [PMID: 29421038 DOI: 10.1016/j.enzmictec.2017.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/27/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
Abstract
In this study, we report the production of uracil from methanol by an isolated methylotrophic bacterium, Methylobacterium sp. WJ4. The use of methanol as alternative carbon feedstock is attractive option in biotechnology. As a feedstock of biotechnological processes, methanol has distinct advantages over methane. This is not only due to physical and chemical considerations, but also to the properties of the pertinent organisms. Besides, with a wide array of biological activities and synthetic accessibility, uracil is considered as privileged structures in drug discovery. Uracil analogues have been applied to treatments of patients with cancer or viral infections. In this respect, it is meaningful to produce uracil using methanol. The effect of process parameters and methanol concentration for uracil production were investigated and optimized. Uracil production was remarkably increased to 5.76mgg cell dry weight-1 in optimized condition. The results were significant for further understanding of methylotrophic bacteria on uracil production.
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Affiliation(s)
- Wangjun Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Sangwoo Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Insu Song
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Yuhyun Kwon
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Soohyun Park
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Byung-Keun Oh
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Jinwon Lee
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea.
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71
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Schada von Borzyskowski L, Sonntag F, Pöschel L, Vorholt JA, Schrader J, Erb TJ, Buchhaupt M. Replacing the Ethylmalonyl-CoA Pathway with the Glyoxylate Shunt Provides Metabolic Flexibility in the Central Carbon Metabolism of Methylobacterium extorquens AM1. ACS Synth Biol 2018; 7:86-97. [PMID: 29216425 DOI: 10.1021/acssynbio.7b00229] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ethylmalonyl-CoA pathway (EMCP) is an anaplerotic reaction sequence in the central carbon metabolism of numerous Proteo- and Actinobacteria. The pathway features several CoA-bound mono- and dicarboxylic acids that are of interest as platform chemicals for the chemical industry. The EMCP, however, is essential for growth on C1 and C2 carbon substrates and therefore cannot be simply interrupted to drain these intermediates. In this study, we aimed at reengineering central carbon metabolism of the Alphaproteobacterium Methylobacterium extorquens AM1 for the specific production of EMCP derivatives in the supernatant. Establishing a heterologous glyoxylate shunt in M. extorquens AM1 restored wild type-like growth in several EMCP knockout strains on defined minimal medium with acetate as carbon source. We further engineered one of these strains that carried a deletion of the gene encoding crotonyl-CoA carboxylase/reductase to demonstrate in a proof-of-concept the specific production of crotonic acid in the supernatant on a defined minimal medium. Our experiments demonstrate that it is in principle possible to further exploit the EMCP by establishing an alternative central carbon metabolic pathway in M. extorquens AM1, opening many possibilities for the biotechnological production of EMCP-derived compounds in future.
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Affiliation(s)
| | - Frank Sonntag
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Laura Pöschel
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Jens Schrader
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
| | - Tobias J. Erb
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
- Center for Synthetic Microbiology, SYNMIKRO, 35043 Marburg, Germany
| | - Markus Buchhaupt
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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72
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Ueoka R, Bortfeld-Miller M, Morinaka BI, Vorholt JA, Piel J. Toblerols: Cyclopropanol-Containing Polyketide Modulators of Antibiosis in Methylobacteria. Angew Chem Int Ed Engl 2017; 57:977-981. [PMID: 29112783 DOI: 10.1002/anie.201709056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Indexed: 11/11/2022]
Abstract
Trans-AT polyketide synthases (PKSs) are a family of biosynthetically versatile modular type I PKSs that generate bioactive polyketides of impressive structural diversity. In this study, we detected, in the genome of several bacteria a cryptic, architecturally unusual trans-AT PKS gene cluster which eluded automated PKS prediction. Genomic mining of one of these strains, the model methylotroph Methylobacterium extorquens AM1, revealed unique epoxide- and cyclopropanol-containing polyketides named toblerols. Relative and absolute stereochemistry were determined by NMR experiments, chemical derivatization, and the comparison of CD data between the derivatized natural product and a synthesized model compound. Biosynthetic data suggest that the cyclopropanol moiety is generated by carbon-carbon shortening of a more extended precursor. Surprisingly, a knock-out strain impaired in polyketide production showed strong inhibitory activity against other methylobacteria in contrast to the wild-type producer. The activity was inhibited by complementation with toblerols, thus suggesting that these compounds modulate an as-yet unknown methylobacterial antibiotic.
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Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Brandon I Morinaka
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland.,Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Julia A Vorholt
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eigenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
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73
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Ueoka R, Bortfeld-Miller M, Morinaka BI, Vorholt JA, Piel J. Toblerols: Cyclopropanol-Containing Polyketide Modulators of Antibiosis in Methylobacteria. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Reiko Ueoka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Brandon I. Morinaka
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
- Department of Pharmacy; National University of Singapore; 18 Science Drive 4 Singapore 117543 Singapore
| | - Julia A. Vorholt
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
| | - Jörn Piel
- Institute of Microbiology; Eigenössische Technische Hochschule (ETH) Zurich; Vladimir-Prelog-Weg 1-5/10 8093 Zurich Switzerland
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74
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Bringel F, Vuilleumier S. Metabolic Regulation: A Master Role for Ribulose-1,5-Bisphosphate in One-Carbon Assimilation. Curr Biol 2017; 27:R1127-R1129. [PMID: 29065298 DOI: 10.1016/j.cub.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Engineering organisms for biotechnology applications requires knowledge of their essential genes and associated regulatory networks. A new study of methylotrophic metabolism in Methylobacterium reveals essentiality of the unregulated, off-pathway phosphoribulokinase gene and an unexpected key regulatory role for its product ribulose-1,5-bisphosphate.
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Affiliation(s)
- Françoise Bringel
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France.
| | - Stéphane Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Department of Microbiology, Genomics and the Environment, Strasbourg, France
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75
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Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S, Bringel F. Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium. Front Microbiol 2017; 8:1600. [PMID: 28919881 PMCID: PMC5585157 DOI: 10.3389/fmicb.2017.01600] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.
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Affiliation(s)
- Pauline Chaignaud
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France.,Department of Ecological Microbiology, University of BayreuthBayreuth, Germany
| | - Bruno Maucourt
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Marion Weiman
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Adriana Alberti
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Steffen Kolb
- Department of Ecological Microbiology, University of BayreuthBayreuth, Germany.,Institute of Landscape Biogeochemistry-Leibniz Centre for Agricultural Landscape Research (ZALF)Müncheberg, Germany
| | - Stéphane Cruveiller
- UMR 8030 Centre National de la Recherche Scientifique-CEA, DSV/IG/Genoscope, LABGeMEvry, France
| | - Stéphane Vuilleumier
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
| | - Françoise Bringel
- Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France
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Transposon Sequencing Uncovers an Essential Regulatory Function of Phosphoribulokinase for Methylotrophy. Curr Biol 2017; 27:2579-2588.e6. [PMID: 28823675 DOI: 10.1016/j.cub.2017.07.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/04/2017] [Accepted: 07/11/2017] [Indexed: 11/21/2022]
Abstract
Methylotrophy is the ability of organisms to grow at the expense of reduced one-carbon compounds, such as methanol or methane. Here, we used transposon sequencing combining hyper-saturated transposon mutagenesis with high-throughput sequencing to define the essential methylotrophy genome of Methylobacterium extorquens PA1, a model methylotroph. To distinguish genomic regions required for growth only on methanol from general required genes, we contrasted growth on methanol with growth on succinate, a non-methylotrophic reference substrate. About 500,000 insertions were mapped for each condition, resulting in a median insertion distance of five base pairs. We identified 147 genes and 76 genes as specific for growth on methanol and succinate, respectively, and a set of 590 genes as required under both growth conditions. For the integration of metabolic functions, we reconstructed a genome-scale metabolic model and performed in silico essentiality analysis. In total, the approach uncovered 95 genes not previously described as crucial for methylotrophy, including genes involved in respiration, carbon metabolism, transport, and regulation. Strikingly, regardless of the absence of the Calvin cycle in the methylotroph, the screen led to the identification of the gene for phosphoribulokinase as essential during growth on methanol, but not during growth on succinate. Genetic experiments in addition to metabolomics and proteomics revealed that phosphoribulokinase serves a key regulatory function. Our data support a model according to which ribulose-1,5-bisphosphate is an essential metabolite that induces a transcriptional regulator driving one-carbon assimilation.
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77
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Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21. GENOME ANNOUNCEMENTS 2017; 5:5/30/e00622-17. [PMID: 28751386 PMCID: PMC5532824 DOI: 10.1128/genomea.00622-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The genome sequence of Hyphomicrobium sp. strain GJ21, isolated in the Netherlands from samples of environments contaminated with halogenated pollutants and capable of using dichloromethane as its sole carbon and energy source, was determined.
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78
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Tlusty M, Rhyne A, Szczebak JT, Bourque B, Bowen JL, Burr G, Marx CJ, Feinberg L. A transdisciplinary approach to the initial validation of a single cell protein as an alternative protein source for use in aquafeeds. PeerJ 2017; 5:e3170. [PMID: 28413727 PMCID: PMC5390762 DOI: 10.7717/peerj.3170] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/12/2017] [Indexed: 01/12/2023] Open
Abstract
The human population is growing and, globally, we must meet the challenge of increased protein needs required to feed this population. Single cell proteins (SCP), when coupled to aquaculture production, offer a means to ensure future protein needs can be met without direct competition with food for people. To demonstrate a given type of SCP has potential as a protein source for use in aquaculture feed, a number of steps need to be validated including demonstrating that the SCP is accepted by the species in question, leads to equivalent survival and growth, does not result in illness or other maladies, is palatable to the consumer, is cost effective to produce and can easily be incorporated into diets using existing technology. Here we examine white shrimp (Litopenaeus vannamei) growth and consumer taste preference, smallmouth grunt (Haemulon chrysargyreum) growth, survival, health and gut microbiota, and Atlantic salmon (Salmo salar) digestibility when fed diets that substitute the bacterium Methylobacterium extorquens at a level of 30% (grunts), 100% (shrimp), or 55% (salmon) of the fishmeal in a compound feed. In each of these tests, animals performed equivalently when fed diets containing M. extorquens as when fed a standard aquaculture diet. This transdisciplinary approach is a first validation of this bacterium as a potential SCP protein substitute in aquafeeds. Given the ease to produce this SCP through an aerobic fermentation process, the broad applicability for use in aquaculture indicates the promise of M. extorquens in leading toward greater food security in the future.
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Affiliation(s)
- Michael Tlusty
- Anderson Cabot Center for Ocean Life at the New England Aquarium, New England Aquarium, Boston, MA, United States.,School for the Environment, University of Massachusetts Boston, Boston, MA, USA
| | - Andrew Rhyne
- Anderson Cabot Center for Ocean Life at the New England Aquarium, New England Aquarium, Boston, MA, United States.,School for the Environment, University of Massachusetts Boston, Boston, MA, USA.,Department of Arts and Sciences, Roger Williams University, Bristol, RI, United States.,Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, United States
| | - Joseph T Szczebak
- Department of Biology and Marine Biology, Roger Williams University, Bristol, Rhode Island, United States
| | - Bradford Bourque
- Department of Arts and Sciences, Roger Williams University, Bristol, RI, United States
| | | | - Gary Burr
- National Cold Water Marine Aquaculture Center, USDA ARS, Franklin, ME, United States
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79
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Nærdal I, Netzer R, Irla M, Krog A, Heggeset TMB, Wendisch VF, Brautaset T. l-lysine production by Bacillus methanolicus: Genome-based mutational analysis and l-lysine secretion engineering. J Biotechnol 2017; 244:25-33. [PMID: 28163092 DOI: 10.1016/j.jbiotec.2017.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 01/06/2017] [Accepted: 02/01/2017] [Indexed: 10/20/2022]
Abstract
Bacillus methanolicus is a methylotrophic bacterium with an increasing interest in academic research and for biotechnological applications. This bacterium was previously applied for methanol-based production of l-glutamate, l-lysine and the five-carbon diamine cadaverine by wild type, classical mutant and recombinant strains. The genomes of two different l-lysine secreting B. methanolicus classical mutant strains, NOA2#13A52-8A66 and M168-20, were sequenced. We focused on mutational mapping in genes present in l-lysine and other relevant amino acid biosynthetic pathways, as well as in the primary cell metabolism important for precursor supply. In addition to mutations in the aspartate pathway genes dapG, lysA and hom-1, new mutational target genes like alr, proA, proB1, leuC, odhA and pdhD were identified. Surprisingly, no mutations were found in the putative l-lysine transporter gene lysEMGA3. Inspection of the wild type B. methanolicus strain PB1 genome sequence identified two homologous putative l-lysine transporter genes, lysEPB1 and lysE2PB1. The biological role of these putative l-lysine transporter genes, together with the heterologous l-lysine exporter gene lysECg from Corynebacterium glutamicum, were therefore investigated. Our results demonstrated that the titer of secreted l-lysine in B. methanolicus was significantly increased by overexpression of lysECg while overexpression of lysEMGA3, lysEPB1 and lysE2PB1 had no measurable effect.
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Affiliation(s)
- Ingemar Nærdal
- SINTEF Materials and Chemistry, Department of Biotechnology and Nanomedicine, Trondheim, Norway
| | - Roman Netzer
- SINTEF Materials and Chemistry, Department of Biotechnology and Nanomedicine, Trondheim, Norway
| | - Marta Irla
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Anne Krog
- SINTEF Materials and Chemistry, Department of Biotechnology and Nanomedicine, Trondheim, Norway
| | | | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Bielefeld, Germany
| | - Trygve Brautaset
- NTNU, Norwegian University of Science and Technology, Department of Biotechnology, Trondheim, Norway.
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Synthetic metabolism: metabolic engineering meets enzyme design. Curr Opin Chem Biol 2017; 37:56-62. [PMID: 28152442 DOI: 10.1016/j.cbpa.2016.12.023] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 01/29/2023]
Abstract
Metabolic engineering aims at modifying the endogenous metabolic network of an organism to harness it for a useful biotechnological task, for example, production of a value-added compound. Several levels of metabolic engineering can be defined and are the topic of this review. Basic 'copy, paste and fine-tuning' approaches are limited to the structure of naturally existing pathways. 'Mix and match' approaches freely recombine the repertoire of existing enzymes to create synthetic metabolic networks that are able to outcompete naturally evolved pathways or redirect flux toward non-natural products. The space of possible metabolic solution can be further increased through approaches including 'new enzyme reactions', which are engineered on the basis of known enzyme mechanisms. Finally, by considering completely 'novel enzyme chemistries' with de novo enzyme design, the limits of nature can be breached to derive the most advanced form of synthetic pathways. We discuss the challenges and promises associated with these different metabolic engineering approaches and illuminate how enzyme engineering is expected to take a prime role in synthetic metabolic engineering for biotechnology, chemical industry and agriculture of the future.
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81
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Pattnaik S, Rajkumari J, Paramanandham P, Busi S. Indole Acetic Acid Production and Growth-Promoting Activity of Methylobacterium extorquens MP1 and Methylobacterium zatmanii MS4 in Tomato. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/19315260.2017.1283381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Subhaswaraj Pattnaik
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Jobina Rajkumari
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | | | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
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82
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Production of 2-Hydroxyisobutyric Acid from Methanol by Methylobacterium extorquens AM1 Expressing (R)-3-Hydroxybutyryl Coenzyme A-Isomerizing Enzymes. Appl Environ Microbiol 2017; 83:AEM.02622-16. [PMID: 27836853 DOI: 10.1128/aem.02622-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 01/05/2023] Open
Abstract
The biotechnological production of the methyl methacrylate precursor 2-hydroxyisobutyric acid (2-HIBA) via bacterial poly-3-hydroxybutyrate (PHB) overflow metabolism requires suitable (R)-3-hydroxybutyryl coenzyme A (CoA)-specific coenzyme B12-dependent mutases (RCM). Here, we characterized a predicted mutase from Bacillus massiliosenegalensis JC6 as a mesophilic RCM closely related to the thermophilic enzyme previously identified in Kyrpidia tusciae DSM 2912 (M.-T. Weichler et al., Appl Environ Microbiol 81:4564-4572, 2015, https://doi.org/10.1128/AEM.00716-15). Using both RCM variants, 2-HIBA production from methanol was studied in fed-batch bioreactor experiments with recombinant Methylobacterium extorquens AM1. After complete nitrogen consumption, the concomitant formation of PHB and 2-HIBA was achieved, indicating that both sets of RCM genes were successfully expressed. However, although identical vector systems and incubation conditions were chosen, the metabolic activity of the variant bearing the RCM genes from strain DSM 2912 was severely inhibited, likely due to the negative effects caused by heterologous expression. In contrast, the biomass yield of the variant expressing the JC6 genes was close to the wild-type performance, and 2-HIBA titers of 2.1 g liter-1 could be demonstrated. In this case, up to 24% of the substrate channeled into overflow metabolism was converted to the mutase product, and maximal combined 2-HIBA plus PHB yields from methanol of 0.11 g g-1 were achieved. Reverse transcription-quantitative PCR analysis revealed that metabolic genes, such as methanol dehydrogenase and acetoacetyl-CoA reductase genes, are strongly downregulated after exponential growth, which currently prevents a prolonged overflow phase, thus preventing higher product yields with strain AM1. IMPORTANCE In this study, we genetically modified a methylotrophic bacterium in order to channel intermediates of its overflow metabolism to the C4 carboxylic acid 2-hydroxyisobutyric acid, a precursor of acrylic glass. This has implications for biotechnology, as it shows that reduced C1 substrates, such as methanol and formic acid, can be alternative feedstocks for producing today's commodities. We found that product titers and yields depend more on host physiology than on the activity of the introduced heterologous function modifying the overflow metabolism. In addition, we show that the fitness of recombinant strains substantially varies when they express orthologous genes from different origins. Further studies are needed to extend the overflow production phase in methylotrophic microorganisms for the implementation of biotechnological processes.
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83
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Zhang W, Zhang T, Wu S, Wu M, Xin F, Dong W, Ma J, Zhang M, Jiang M. Guidance for engineering of synthetic methylotrophy based on methanol metabolism in methylotrophy. RSC Adv 2017. [DOI: 10.1039/c6ra27038g] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Methanol represents an attractive non-food raw material in biotechnological processes from an economic and process point of view. It is vital to elucidate methanol metabolic pathways, which will help to genetically construct non-native methylotrophs.
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Affiliation(s)
- Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Ting Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Sihua Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Mingke Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Min Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering
- College of Biotechnology and Pharmaceutical Engineering
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)
- Nanjing Tech University
- Nanjing
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84
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Wendisch VF, Brito LF, Gil Lopez M, Hennig G, Pfeifenschneider J, Sgobba E, Veldmann KH. The flexible feedstock concept in Industrial Biotechnology: Metabolic engineering of Escherichia coli, Corynebacterium glutamicum, Pseudomonas, Bacillus and yeast strains for access to alternative carbon sources. J Biotechnol 2016; 234:139-157. [DOI: 10.1016/j.jbiotec.2016.07.022] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
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85
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Müller DB, Schubert OT, Röst H, Aebersold R, Vorholt JA. Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization. Mol Cell Proteomics 2016; 15:3256-3269. [PMID: 27457762 DOI: 10.1074/mcp.m116.058164] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 12/24/2022] Open
Abstract
Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals species-specific adaptations to the host environment and provide evidence for niche separation within the plant microbiota.
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Affiliation(s)
- Daniel B Müller
- From the ‡Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland
| | - Olga T Schubert
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Hannes Röst
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; ¶Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- From the ‡Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland;
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86
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Cui J, Good NM, Hu B, Yang J, Wang Q, Sadilek M, Yang S. Metabolomics Revealed an Association of Metabolite Changes and Defective Growth in Methylobacterium extorquens AM1 Overexpressing ecm during Growth on Methanol. PLoS One 2016; 11:e0154043. [PMID: 27116459 PMCID: PMC4846091 DOI: 10.1371/journal.pone.0154043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/07/2016] [Indexed: 11/18/2022] Open
Abstract
Methylobacterium extorquens AM1 is a facultative methylotroph capable of growth on both single-carbon and multi-carbon compounds. The ethylmalonyl-CoA (EMC) pathway is one of the central assimilatory pathways in M. extorquens during growth on C1 and C2 substrates. Previous studies had shown that ethylmalonyl-CoA mutase functioned as a control point during the transition from growth on succinate to growth on ethylamine. In this study we overexpressed ecm, phaA, mcmAB and found that upregulating ecm by expressing it from the strong constitutive mxaF promoter caused a 27% decrease in growth rate on methanol compared to the strain with an empty vector. Targeted metabolomics demonstrated that most of the central intermediates in the ecm over-expressing strain did not change significantly compared to the control strain; However, poly-β-hydroxybutyrate (PHB) was 4.5-fold lower and 3-hydroxybutyryl-CoA was 1.6-fold higher. Moreover, glyoxylate, a toxic and highly regulated essential intermediate, was determined to be 2.6-fold higher when ecm was overexpressed. These results demonstrated that overexpressing ecm can manipulate carbon flux through the EMC pathway and divert it from the carbon and energy storage product PHB, leading to an accumulation of glyoxylate. Furthermore, untargeted metabolomics discovered two unusual metabolites, alanine (Ala)-meso-diaminopimelic acid (mDAP) and Ala-mDAP-Ala, each over 45-fold higher in the ecm over-expressing strain. These two peptides were also found to be highly produced in a dose-dependent manner when glyoxylate was added to the control strain. Overall, this work has explained a direct association of ecm overexpression with glyoxylate accumulation up to a toxic level, which inhibits cell growth on methanol. This research provides useful insight for manipulating the EMC pathway for efficiently producing high-value chemicals in M. extorquens.
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Affiliation(s)
- Jinyu Cui
- School of Life Science, Qingdao Agricultural University, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao, Shandong Province, China
| | - Nathan M. Good
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Bo Hu
- Kemin Industries, KI Research & Development, Des Moines, Iowa, United States of America
| | - Jing Yang
- School of Life Science, Qingdao Agricultural University, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao, Shandong Province, China
| | - Qianwen Wang
- Central Laboratory, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Song Yang
- School of Life Science, Qingdao Agricultural University, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao, Shandong Province, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
- * E-mail:
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Rohde MT, Paufler S, Harms H, Maskow T. Calorespirometric feeding control enhances bioproduction from toxic feedstocks-Demonstration for biopolymer production out of methanol. Biotechnol Bioeng 2016; 113:2113-21. [PMID: 27043974 DOI: 10.1002/bit.25986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/02/2016] [Accepted: 03/30/2016] [Indexed: 11/08/2022]
Abstract
The sustainable production of fuels and industrial bulk chemicals by microorganisms in biotechnological processes is promising but still facing various challenges. In particular, toxic substrates require an efficient process control strategy. Methanol, as an example, has the potential to become a major future feedstock due to its availability from fossil and renewable resources. However, besides being toxic, methanol is highly volatile. To optimize its dosage during microbial cultivations, an innovative, predictive process control strategy based on calorespirometry, i.e., simultaneous measurements of heat and CO2 emission rates, was developed. This rarely used technique allows an online-estimation of growth parameters such as the specific growth rate and substrate consumption rate as well as a detection of shifts in microbial metabolism thus enabling an adapted feeding for different phases of growth. The calorespirometric control strategy is demonstrated exemplarily for growth of the methylotrophic bacterium Methylobacterium extorquens on methanol and compared to alternative control strategies. Applying the new approach, the methanol concentration could be maintained far below a critical limit, while increased growth rates of M. extorquens and higher final contents of the biopolymer polyhydroxybutyrate were obtained. Biotechnol. Bioeng. 2016;113: 2113-2121. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Maria-Teresa Rohde
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sven Paufler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Thomas Maskow
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.
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88
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Lanthanide-Dependent Regulation of Methanol Oxidation Systems in Methylobacterium extorquens AM1 and Their Contribution to Methanol Growth. J Bacteriol 2016; 198:1250-9. [PMID: 26833413 DOI: 10.1128/jb.00937-15] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/28/2016] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED Methylobacterium extorquens AM1 has two distinct types of methanol dehydrogenase (MeDH) enzymes that catalyze the oxidation of methanol to formaldehyde. MxaFI-MeDH requires pyrroloquinoline quinone (PQQ) and Ca in its active site, while XoxF-MeDH requires PQQ and lanthanides, such as Ce and La. Using MeDH mutant strains to conduct growth analysis and MeDH activity assays, we demonstrate that M. extorquens AM1 has at least one additional lanthanide-dependent methanol oxidation system contributing to methanol growth. Additionally, the abilities of different lanthanides to support growth were tested and strongly suggest that both XoxF and the unknown methanol oxidation system are able to use La, Ce, Pr, Nd, and, to some extent, Sm. Further, growth analysis using increasing La concentrations showed that maximum growth rate and yield were achieved at and above 1 μM La, while concentrations as low as 2.5 nM allowed growth at a reduced rate. Contrary to published data, we show that addition of exogenous lanthanides results in differential expression from the xox1 and mxa promoters, upregulating genes in the xox1 operon and repressing genes in the mxa operon. Using transcriptional reporter fusions, intermediate expression from both the mxa and xox1 promoters was detected when 50 to 100 nM La was added to the growth medium, suggesting that a condition may exist under which M. extorquens AM1 is able to utilize both enzymes simultaneously. Together, these results suggest that M. extorquens AM1 actively senses and responds to lanthanide availability, preferentially utilizing the lanthanide-dependent MeDHs when possible. IMPORTANCE The biological role of lanthanides is a nascent field of study with tremendous potential to impact many areas in biology. Our studies demonstrate that there is at least one additional lanthanide-dependent methanol oxidation system, distinct from the MxaFI and XoxF MeDHs, that may aid in classifying additional environmental organisms as methylotrophs. Further, our data suggest that M. extorquens AM1 has a mechanism to regulate which MeDH is transcribed, depending on the presence or absence of lanthanides. While the mechanism controlling differential regulation is not yet understood, further research into how methylotrophs obtain and use lanthanides will facilitate their cultivation in the laboratory and their use as a biomining and biorecycling strategy for recovery of these commercially valuable rare-earth elements.
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89
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Hu B, Yang YM, Beck DAC, Wang QW, Chen WJ, Yang J, Lidstrom ME, Yang S. Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:84. [PMID: 27069508 PMCID: PMC4827201 DOI: 10.1186/s13068-016-0497-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/25/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND The toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. However, M. extorquens AM1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. Only a few studies have reported the general stress response of M. extorquens AM1 to solvent stress. Therefore, it is highly desirable to obtain a strain with ameliorated 1-butanol tolerance and elucidate the molecular mechanism of 1-butnaol tolerance in M. extorquens AM1 for future strain improvement. RESULTS In this work, adaptive laboratory evolution was used as a tool to isolate mutants with 1-butanol tolerance up to 0.5 %. The evolved strains, BHBT3 and BHBT5, demonstrated increased growth rates and higher survival rates with the existence of 1-butanol. Whole genome sequencing revealed a SNP mutation at kefB in BHBT5, which was confirmed to be responsible for increasing 1-butanol tolerance through an allelic exchange experiment. Global metabolomic analysis further discovered that the pools of multiple key metabolites, including fatty acids, amino acids, and disaccharides, were increased in BHBT5 in response to 1-butanol stress. Additionally, the carotenoid synthesis pathway was significantly down-regulated in BHBT5. CONCLUSIONS We successfully screened mutants resistant to 1-butanol and provided insights into the molecular mechanism of 1-butanol tolerance in M. extorquens AM1. This research will be useful for uncovering the mechanism of cellular response of M. extorquens AM1 to solvent stress, and will provide the genetic blueprint for the rational design of a strain of M. extorquens AM1 with increased 1-butanol tolerance in the future.
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Affiliation(s)
- Bo Hu
- />Department of Chemical Engineering, University of Washington, Seattle, WA USA
- />Industrial Product Division, Intrexon Corporation, South San Francisco, CA 94080 USA
| | - Yi-Ming Yang
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - David A. C. Beck
- />Department of Chemical Engineering, University of Washington, Seattle, WA USA
- />eScience Institute, University of Washington, Seattle, WA USA
| | - Qian-Wen Wang
- />Central Laboratory, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - Wen-Jing Chen
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - Jing Yang
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
| | - Mary E. Lidstrom
- />Department of Chemical Engineering, University of Washington, Seattle, WA USA
- />Department of Microbiology, University of Washington, Seattle, WA 98195-1750 USA
| | - Song Yang
- />School of Life Science, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province China
- />Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
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90
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Firsova YE, Torgonskaya ML, Trotsenko YA. Functionality of the xoxF gene in Methylobacterium dichloromethanicum DM4. Microbiology (Reading) 2015. [DOI: 10.1134/s002626171506003x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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91
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Alamgir KM, Masuda S, Fujitani Y, Fukuda F, Tani A. Production of ergothioneine by Methylobacterium species. Front Microbiol 2015; 6:1185. [PMID: 26579093 PMCID: PMC4621440 DOI: 10.3389/fmicb.2015.01185] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 10/12/2015] [Indexed: 01/09/2023] Open
Abstract
Metabolomic analysis revealed that Methylobacterium cells accumulate a large amount of ergothioneine (EGT), which is a sulfur-containing, non-proteinogenic, antioxidative amino acid derived from histidine. EGT biosynthesis and its role in methylotrophy and physiology for plant surface-symbiotic Methylobacterium species were investigated in this study. Almost all Methylobacterium type strains can synthesize EGT. We selected one of the most productive strains (M. aquaticum strain 22A isolated from a moss), and investigated the feasibility of fermentative EGT production through optimization of the culture condition. Methanol as a carbon source served as the best substrate for production. The productivity reached up to 1000 μg/100 ml culture (1200 μg/g wet weight cells, 6.3 mg/g dry weight) in 38 days. Next, we identified the genes (egtBD) responsible for EGT synthesis, and generated a deletion mutant defective in EGT production. Compared to the wild type, the mutant showed better growth on methanol and on the plant surface as well as severe susceptibility to heat treatment and irradiation of ultraviolet (UV) and sunlight. These results suggested that EGT is not involved in methylotrophy, but is involved in their phyllospheric lifestyle fitness of the genus in natural conditions.
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Affiliation(s)
- Kabir M Alamgir
- Group of Plant-Microbe Interactions, Institute of Plant Science and Resources, Okayama University Okayama, Japan
| | - Sachiko Masuda
- Group of Plant-Microbe Interactions, Institute of Plant Science and Resources, Okayama University Okayama, Japan ; Advanced Low Carbon Technology Research and Development Program, Japan Science and Technology Agency Tokyo, Japan
| | - Yoshiko Fujitani
- Group of Plant-Microbe Interactions, Institute of Plant Science and Resources, Okayama University Okayama, Japan
| | - Fumio Fukuda
- Laboratory of Pomology, Graduate School of Environmental and Life Science, Okayama University Okayama, Japan
| | - Akio Tani
- Group of Plant-Microbe Interactions, Institute of Plant Science and Resources, Okayama University Okayama, Japan
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92
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Xia F, Zou B, Shen C, Zhu T, Gao XH, Quan ZX. Complete genome sequence of Methylophilus sp. TWE2 isolated from methane oxidation enrichment culture of tap-water. J Biotechnol 2015; 211:121-2. [DOI: 10.1016/j.jbiotec.2015.07.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/28/2022]
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93
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Christen M, Deutsch S, Christen B. Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis. ACS Synth Biol 2015; 4:927-34. [PMID: 26107775 DOI: 10.1021/acssynbio.5b00087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent advances in synthetic biology have resulted in an increasing demand for the de novo synthesis of large-scale DNA constructs. Any process improvement that enables fast and cost-effective streamlining of digitized genetic information into fabricable DNA sequences holds great promise to study, mine, and engineer genomes. Here, we present Genome Calligrapher, a computer-aided design web tool intended for whole genome refactoring of bacterial chromosomes for de novo DNA synthesis. By applying a neutral recoding algorithm, Genome Calligrapher optimizes GC content and removes obstructive DNA features known to interfere with the synthesis of double-stranded DNA and the higher order assembly into large DNA constructs. Subsequent bioinformatics analysis revealed that synthesis constraints are prevalent among bacterial genomes. However, a low level of codon replacement is sufficient for refactoring bacterial genomes into easy-to-synthesize DNA sequences. To test the algorithm, 168 kb of synthetic DNA comprising approximately 20 percent of the synthetic essential genome of the cell-cycle bacterium Caulobacter crescentus was streamlined and then ordered from a commercial supplier of low-cost de novo DNA synthesis. The successful assembly into eight 20 kb segments indicates that Genome Calligrapher algorithm can be efficiently used to refactor difficult-to-synthesize DNA. Genome Calligrapher is broadly applicable to recode biosynthetic pathways, DNA sequences, and whole bacterial genomes, thus offering new opportunities to use synthetic biology tools to explore the functionality of microbial diversity. The Genome Calligrapher web tool can be accessed at https://christenlab.ethz.ch/GenomeCalligrapher .
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Affiliation(s)
- Matthias Christen
- Institute
of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland
| | - Samuel Deutsch
- Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Beat Christen
- Institute
of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland
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94
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Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Appl Microbiol Biotechnol 2015; 99:10163-76. [PMID: 26276544 DOI: 10.1007/s00253-015-6906-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
Abstract
Methanol, a one-carbon compound, can be utilized by a variety of bacteria and other organisms as carbon and energy source and is regarded as a promising substrate for biotechnological production. In this study, a strain of non-methylotrophic Corynebacterium glutamicum, which was able to produce the polyamide building block cadaverine as non-native product, was engineered for co-utilization of methanol. Expression of the gene encoding NAD+-dependent methanol dehydrogenase (Mdh) from the natural methylotroph Bacillus methanolicus increased methanol oxidation. Deletion of the endogenous aldehyde dehydrogenase genes ald and fadH prevented methanol oxidation to carbon dioxide and formaldehyde detoxification via the linear formaldehyde dissimilation pathway. Heterologous expression of genes for the key enzymes hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase of the ribulose monophosphate (RuMP) pathway in this strain restored growth in the presence of methanol or formaldehyde, which suggested efficient formaldehyde detoxification involving RuMP key enzymes. While growth with methanol as sole carbon source was not observed, the fate of 13C-methanol added as co-substrate to sugars was followed and the isotopologue distribution indicated incorporation into central metabolites and in vivo activity of the RuMP pathway. In addition, 13C-label from methanol was traced to the secreted product cadaverine. Thus, this synthetic biology approach led to a C. glutamicum strain that converted the non-natural carbon substrate methanol at least partially to the non-native product cadaverine.
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95
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Carroll SM, Chubiz LM, Agashe D, Marx CJ. Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1. Microorganisms 2015; 3:152-74. [PMID: 27682084 PMCID: PMC5023240 DOI: 10.3390/microorganisms3020152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety in the numbers and types of mutations that occurred, including instances of parallel mutations at targets that may have been "rationalized" by the bioengineer, plus other "illogical" mutations that demonstrate the ability of evolution to expose unforeseen optimization solutions. Notably, we investigated mutations to RNA polymerase, which provided a massive growth benefit but are linked to highly aberrant transcriptional profiles. Overall, we highlight the power of experimental evolution to present genetic and physiological solutions for strain optimization, particularly in systems where the challenges of engineering are too many or too difficult to overcome via traditional engineering methods.
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Affiliation(s)
- Sean Michael Carroll
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lon M Chubiz
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63103, USA.
| | - Deepa Agashe
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- National Centre for Biological Sciences, Bangalore 560065, India.
| | - Christopher J Marx
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83843, USA.
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96
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Dourado MN, Aparecida Camargo Neves A, Santos DS, Araújo WL. Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp. BIOMED RESEARCH INTERNATIONAL 2015; 2015:909016. [PMID: 25861650 PMCID: PMC4377440 DOI: 10.1155/2015/909016] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/31/2014] [Accepted: 01/29/2015] [Indexed: 11/17/2022]
Abstract
The genus Methylobacterium is composed of pink-pigmented facultative methylotrophic (PPFM) bacteria, which are able to synthesize carotenoids and grow on reduced organic compounds containing one carbon (C1), such as methanol and methylamine. Due to their high phenotypic plasticity, these bacteria are able to colonize different habitats, such as soil, water, and sediment, and different host plants as both endophytes and epiphytes. In plant colonization, the frequency and distribution may be influenced by plant genotype or by interactions with other associated microorganisms, which may result in increasing plant fitness. In this review, different aspects of interactions with the host plant are discussed, including their capacity to fix nitrogen, nodule the host plant, produce cytokinins, auxin and enzymes involved in the induction of systemic resistance, such as pectinase and cellulase, and therefore plant growth promotion. In addition, bacteria belonging to this group can be used to reduce environmental contamination because they are able to degrade toxic compounds, tolerate high heavy metal concentrations, and increase plant tolerance to these compounds. Moreover, genome sequencing and omics approaches have revealed genes related to plant-bacteria interactions that may be important for developing strains able to promote plant growth and protection against phytopathogens.
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Affiliation(s)
| | | | - Daiene Souza Santos
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Welington Luiz Araújo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Brazil
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97
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Sonntag F, Müller JEN, Kiefer P, Vorholt JA, Schrader J, Buchhaupt M. High-level production of ethylmalonyl-CoA pathway-derived dicarboxylic acids by Methylobacterium extorquens under cobalt-deficient conditions and by polyhydroxybutyrate negative strains. Appl Microbiol Biotechnol 2015; 99:3407-19. [PMID: 25661812 DOI: 10.1007/s00253-015-6418-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/15/2015] [Accepted: 01/17/2015] [Indexed: 11/26/2022]
Abstract
Bio-based production of dicarboxylic acids is an emerging research field with remarkable progress during the last decades. The recently established synthesis of the ethylmalonyl-CoA pathway (EMCP)-derived dicarboxylic acids, mesaconic acid and (2S)-methylsuccinic acid, from the alternative carbon source methanol (Sonntag et al., Appl Microbiol Biotechnol 98:4533-4544, 2014) gave a proof of concept for the sustainable production of hitherto biotechnologically inaccessible monomers. In this study, substantial optimizations of the process by different approaches are presented. Abolishment of mesaconic and (2S)-methylsuccinic acid reuptake from culture supernatant and a productivity increase were achieved by 30-fold decreased sodium ion availability in culture medium. Undesired flux from EMCP into polyhydroxybutyrate (PHB) cycle was hindered by the knockout of polyhydroxyalkanoate synthase phaC which was concomitant with 5-fold increased product concentrations. However, frequently occurring suppressors of strain ΔphaC lost their beneficial properties probably due to redirected channeling of acetyl-CoA. Pool sizes of the product precursors were increased by exploiting the presence of two cobalt-dependent mutases in the EMCP: Fine-tuned growth-limiting cobalt concentrations led to 16-fold accumulation of mesaconyl- and (2S)-methylsuccinyl-CoA which in turn resulted in 6-fold increased concentrations of mesaconic and (2S)-methylsuccinic acids, with a combined titer of 0.65 g/l, representing a yield of 0.17 g/g methanol. This work represents an important step toward an industrially relevant production of ethylmalonyl-CoA pathway-derived dicarboxylic acids and the generation of a stable PHB synthesis negative Methylobacterium extorquens strain.
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Affiliation(s)
- Frank Sonntag
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486, Frankfurt am Main, Germany
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98
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Methylotrophy in the thermophilic Bacillus methanolicus, basic insights and application for commodity production from methanol. Appl Microbiol Biotechnol 2014; 99:535-51. [PMID: 25431011 DOI: 10.1007/s00253-014-6224-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/07/2014] [Accepted: 11/08/2014] [Indexed: 01/28/2023]
Abstract
Using methanol as an alternative non-food feedstock for biotechnological production offers several advantages in line with a methanol-based bioeconomy. The Gram-positive, facultative methylotrophic and thermophilic bacterium Bacillus methanolicus is one of the few described microbial candidates with a potential for the conversion of methanol to value-added products. Its capabilities of producing and secreting the commercially important amino acids L-glutamate and L-lysine to high concentrations at 50 °C have been demonstrated and make B. methanolicus a promising target to develop cell factories for industrial-scale production processes. B. methanolicus uses the ribulose monophosphate cycle for methanol assimilation and represents the first example of plasmid-dependent methylotrophy. Recent genome sequencing of two physiologically different wild-type B. methanolicus strains, MGA3 and PB1, accompanied with transcriptome and proteome analyses has generated fundamental new insight into the metabolism of the species. In addition, multiple key enzymes representing methylotrophic and biosynthetic pathways have been biochemically characterized. All this, together with establishment of improved tools for gene expression, has opened opportunities for systems-level metabolic engineering of B. methanolicus. Here, we summarize the current status of its metabolism and biochemistry, available genetic tools, and its potential use in respect to overproduction of amino acids.
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